Abstract
BackgroundPhosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. An earlier study of the PgiC1 gene, which encodes cytosolic PGI in the grass Festuca ovina L., revealed a marked difference in the levels of nucleotide polymorphism between the 5’ and 3’ portions of the gene.MethodsIn the present study, we characterized the sequence polymorphism in F. ovina PgiC1 in more detail and examined possible explanations for the non-uniform pattern of nucleotide polymorphism across the gene.ResultsOur study confirms that the two portions of the PgiC1 gene show substantially different levels of DNA polymorphism and also suggests that the peptide encoded by the 3’ portion of PgiC1 is functionally and structurally more important than that encoded by the 5’ portion. Although there was some evidence of purifying selection (dN/dS test) on the 5’ portion of the gene, the signature of purifying selection was considerably stronger on the 3’ portion of the gene (dN/dS and McDonald–Kreitman tests). Several tests support the action of balancing selection within the 5’ portion of the gene. Wall’s B and Q tests were significant only for the 5’ portion of the gene. There were also marked peaks of nucleotide diversity, Tajima’s D and the dN/dS ratio at or around a PgiC1 codon site (within the 5’ portion of the gene) that a previous study had suggested was subject to positive diversifying selection.ConclusionsOur results suggest that the two portions of the gene have been subject to different selective regimes. Purifying selection appears to have been the main force contributing to the relatively low level of polymorphism within the 3’ portion of the sequence. In contrast, it is possible that balancing selection has contributed to the maintenance of the polymorphism within the 5’ portion of the gene.
Highlights
Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes
The PgiC1 gene, which encodes the cytosolic version of the metabolic enzyme phosphoglucose isomerase (PGI, EC 5.3.1.9), in the grass Festuca ovina L., represents one of the few reported cases in which the levels of nucleotide polymorphism differ substantially between the 3’ and 5’ portions of a gene [18]
The matrix of r2 values (Fig. 3_b) shows that there is a low level of linkage disequilibrium (LD) throughout the entire PgiC1 gene, with no “strong LD” blocks
Summary
Phosphoglucose isomerase (PGI, EC 5.3.1.9) is an essential metabolic enzyme in all eukaryotes. Li et al Hereditas (2017) 154:11 the major histocompatibility complex (MHC) genes These genes are crucial for the ability of a vertebrate host’s immune system to detect evolving pathogens, and it is frequently suggested that the maintenance of the high levels of non-synonymous polymorphism in the MHC gene regions encoding the antigen binding site is a reflection of pathogen-driven balancing selection [15, 16]. The PgiC1 gene, which encodes the cytosolic version of the metabolic enzyme phosphoglucose isomerase (PGI, EC 5.3.1.9), in the grass Festuca ovina L., represents one of the few reported cases in which the levels of nucleotide polymorphism differ substantially between the 3’ and 5’ portions of a gene [18]. Observed differences in enzyme activity between PGI variants in a number of species are consistent with observed associations between the PGI variation and environmental variables or life-history traits – suggesting that the loci coding for PGI may be under selection (e.g. [24, 25])
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